Multiple sequence alignment - TraesCS7B01G142900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G142900 chr7B 100.000 2345 0 0 1 2345 182946643 182944299 0 4331
1 TraesCS7B01G142900 chr3B 92.520 2353 161 14 1 2345 289835205 289837550 0 3356
2 TraesCS7B01G142900 chr3B 92.523 1217 73 16 1143 2345 71910025 71911237 0 1727
3 TraesCS7B01G142900 chr3B 91.742 1211 79 10 1149 2345 128994518 128993315 0 1663
4 TraesCS7B01G142900 chr4B 91.862 2384 147 31 1 2345 486848100 486845725 0 3284
5 TraesCS7B01G142900 chr4B 90.038 2359 213 18 1 2345 207927857 207925507 0 3035
6 TraesCS7B01G142900 chr2B 90.928 2403 150 41 1 2345 405161740 405164132 0 3168
7 TraesCS7B01G142900 chr2B 91.356 2256 174 18 1 2246 575351202 575353446 0 3066
8 TraesCS7B01G142900 chr2B 89.195 1888 161 31 494 2345 279188892 279187012 0 2316
9 TraesCS7B01G142900 chr1B 90.345 2403 166 38 1 2345 475663126 475665520 0 3092
10 TraesCS7B01G142900 chr1B 88.526 2388 224 33 1 2345 534467630 534470010 0 2846
11 TraesCS7B01G142900 chr1B 84.372 2374 309 48 5 2345 298525736 298528080 0 2272


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G142900 chr7B 182944299 182946643 2344 True 4331 4331 100.000 1 2345 1 chr7B.!!$R1 2344
1 TraesCS7B01G142900 chr3B 289835205 289837550 2345 False 3356 3356 92.520 1 2345 1 chr3B.!!$F2 2344
2 TraesCS7B01G142900 chr3B 71910025 71911237 1212 False 1727 1727 92.523 1143 2345 1 chr3B.!!$F1 1202
3 TraesCS7B01G142900 chr3B 128993315 128994518 1203 True 1663 1663 91.742 1149 2345 1 chr3B.!!$R1 1196
4 TraesCS7B01G142900 chr4B 486845725 486848100 2375 True 3284 3284 91.862 1 2345 1 chr4B.!!$R2 2344
5 TraesCS7B01G142900 chr4B 207925507 207927857 2350 True 3035 3035 90.038 1 2345 1 chr4B.!!$R1 2344
6 TraesCS7B01G142900 chr2B 405161740 405164132 2392 False 3168 3168 90.928 1 2345 1 chr2B.!!$F1 2344
7 TraesCS7B01G142900 chr2B 575351202 575353446 2244 False 3066 3066 91.356 1 2246 1 chr2B.!!$F2 2245
8 TraesCS7B01G142900 chr2B 279187012 279188892 1880 True 2316 2316 89.195 494 2345 1 chr2B.!!$R1 1851
9 TraesCS7B01G142900 chr1B 475663126 475665520 2394 False 3092 3092 90.345 1 2345 1 chr1B.!!$F2 2344
10 TraesCS7B01G142900 chr1B 534467630 534470010 2380 False 2846 2846 88.526 1 2345 1 chr1B.!!$F3 2344
11 TraesCS7B01G142900 chr1B 298525736 298528080 2344 False 2272 2272 84.372 5 2345 1 chr1B.!!$F1 2340

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
209 210 0.537188 CAGCGTGGTTACTCCCATCT 59.463 55.0 0.0 0.0 36.74 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2059 0.183492 ATCCCGGGAACATGACATGG 59.817 55.0 30.84 0.44 33.6 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 6.157904 GCCTAGTTCTTACGATCCTTATTCC 58.842 44.000 0.00 0.00 0.00 3.01
126 127 5.702266 TCTTACGATCCTTATTCCAGAGGA 58.298 41.667 0.00 0.00 45.57 3.71
204 205 2.000447 GAATGTCAGCGTGGTTACTCC 59.000 52.381 0.00 0.00 0.00 3.85
209 210 0.537188 CAGCGTGGTTACTCCCATCT 59.463 55.000 0.00 0.00 36.74 2.90
416 417 6.259608 CCACAACAGATTTATTCAGCTCCTAG 59.740 42.308 0.00 0.00 0.00 3.02
616 638 9.973450 TTATTCTAGAGGAAATGAAGAAGATCG 57.027 33.333 0.00 0.00 37.49 3.69
651 673 5.961421 AGAGCTAGTGGAAGAAGTAAGGAAT 59.039 40.000 0.00 0.00 0.00 3.01
805 827 6.099413 TGAGCAAGAGATACCTCAGATTGAAT 59.901 38.462 0.00 0.00 41.87 2.57
1162 1184 4.774726 ACTTTCCTCATGCTAGTCTTGAGA 59.225 41.667 21.14 11.27 45.03 3.27
1200 1222 2.230508 TCCTCGTGTGAGTATTGACCAC 59.769 50.000 0.00 0.00 40.85 4.16
1287 1309 1.519455 CTTGGAGGACATCGACCGC 60.519 63.158 0.00 0.00 0.00 5.68
1543 1577 2.923121 CCCGGTGAGATGTTTCATGAT 58.077 47.619 0.00 0.00 0.00 2.45
1605 1646 2.275880 TGGGTTGCTTAAGCCATGC 58.724 52.632 24.30 11.27 44.57 4.06
1665 1708 5.124297 TGGTGCTTGATGTGAATATGTGAAG 59.876 40.000 0.00 0.00 0.00 3.02
1687 1731 4.275936 AGTGAGTGTTGAATGCCTTGTAAC 59.724 41.667 0.00 0.00 0.00 2.50
1693 1737 5.935789 GTGTTGAATGCCTTGTAACCTAGTA 59.064 40.000 0.00 0.00 0.00 1.82
1716 1760 2.030007 TCTACACAATGCTTGCTTTGCC 60.030 45.455 17.35 0.00 0.00 4.52
1873 1917 5.359009 CCATTGAGAGCAATCACCTAACAAT 59.641 40.000 0.00 0.00 42.66 2.71
2013 2059 2.049888 AGTCCGGCTACCTACAGTAC 57.950 55.000 0.00 0.00 0.00 2.73
2050 2096 1.334869 GATCGGTGGCATGTGAAATCC 59.665 52.381 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.997746 CCTATCAGTTCTTGAACACTTTCCA 59.002 40.000 14.80 0.00 39.77 3.53
80 81 5.360649 ACTAGGCCTATCCTCAAAAACTC 57.639 43.478 14.30 0.00 43.20 3.01
204 205 2.554032 GCCATAACAATCGGGAAGATGG 59.446 50.000 0.00 0.00 40.02 3.51
209 210 3.289407 TCATGCCATAACAATCGGGAA 57.711 42.857 0.00 0.00 0.00 3.97
280 281 9.784531 CCTATATGACATATTCTGGTTTTCAGT 57.215 33.333 13.09 0.00 43.76 3.41
416 417 4.161565 TGTCCTGGTGTTGAGGTATATGAC 59.838 45.833 0.00 0.00 31.85 3.06
594 616 7.057264 TCTCGATCTTCTTCATTTCCTCTAGA 58.943 38.462 0.00 0.00 0.00 2.43
616 638 3.511934 TCCACTAGCTCTTTTCCACTCTC 59.488 47.826 0.00 0.00 0.00 3.20
651 673 4.631377 CCAGCGTTGATGTTCTTCTCAATA 59.369 41.667 0.00 0.00 34.18 1.90
805 827 8.190326 TGTTCCTTGTCTTCTAGTTCATCTTA 57.810 34.615 0.00 0.00 0.00 2.10
1162 1184 8.777413 CACACGAGGATGACATTTATCATTAAT 58.223 33.333 0.00 0.00 39.48 1.40
1200 1222 2.245159 TAGGATGGCAGAAATCAGCG 57.755 50.000 0.00 0.00 0.00 5.18
1287 1309 6.117911 TCACACAAACAACTACAAGTGATG 57.882 37.500 0.00 0.00 30.64 3.07
1343 1368 2.612972 CGAACCTGGTCAGCATGTAGTT 60.613 50.000 0.00 0.00 37.40 2.24
1605 1646 2.524306 TCAGTGGGGCAACATTTAAGG 58.476 47.619 0.00 0.00 39.74 2.69
1665 1708 4.537015 GTTACAAGGCATTCAACACTCAC 58.463 43.478 1.35 0.00 0.00 3.51
1873 1917 5.945784 GGGAACATAGCATGCTAATCCATAA 59.054 40.000 34.67 18.08 34.41 1.90
1998 2043 2.029623 ACATGGTACTGTAGGTAGCCG 58.970 52.381 0.00 0.00 45.30 5.52
2013 2059 0.183492 ATCCCGGGAACATGACATGG 59.817 55.000 30.84 0.44 33.60 3.66
2050 2096 8.428186 TTTATTTATTACTGTCCAAGCTACCG 57.572 34.615 0.00 0.00 0.00 4.02


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.